v1.0.0

v1.0.0 is the release of tidyqpcr after software review and acceptance by rOpenSci.

• removed plot_helper functions 36a16f6
• explicitly use the "by" argument in all joins, updated tests d010f66
• cleaned up tests a113a9a
• fixed urls in README.md 60b354f
• updates to transfer ownership to rOpenSci, including
  • changing all links to point to https://github.com/ropensci/tidyqpcr/ b6b0f2a
  • updating peer review badge, author formatting, fixing dois in the paper, other minor formatting edits

v0.5

Updates to v0.5 in response to rOpenSci review 2nd round. Mostly improvements in documentation and help files, and a change to display_plate functions to make more general and more specialised versions.

• Added missing files to .Rbuildignore and changed references to licence, version and depends in DESCRIPTION ewallace@fa29569
• made packages explicit in tests ewallace@d31933b
• getting started moved in readme c05f925
• Added top-level help-file 98f930b
• Adds read_qpcr_data.R tests f5816f1
• Removes {lifecycle} from description da45200
• Address spelling errors cfe2e7c and 8f354b5
• calculate_dydx_1 to calculate_dydx 45649a1
• changes label_plate_rowcol warnings to notes ba1eb67
• changes display_plate_qpcr() to enable display_plate() to be more general bd482f2. Older code will need to use display_plate_qpcr to ensure that sample_id and target_id info displays.
• improved plot_helpers.R styling 55f4ca5
• Adds basic usage to the Readme 25bed2d
• Updates pkgdown website b88ed9f

Checks, documentation, vignettes, for rOpenSci resubmission

Many improvements, mostly to documentation and vignettes. This release was prepared for resubmission to rOpenSci software review

• Echo setup code chunk in vignettes #137
• Documentation for plate setup avoiding edge wells #132
• Visualizing measurement results in the plate layout in calibration vignette #131
• Fix vignette titles #130
• Reduce package footprint below 5MB by compressing data #128
• Rewrite description of other packages #126
• Tabulate MIQE requirements addressed by tidyqpcr and other R packages #125
• Improved Function documentation #124
• Vignette packages and files, use system.file and explain it #122, #145
• Clarify README #121
• Remove deprecated getdRdTall #103
• Document multi-plate calculations and validate inputs of calculate_drdt_plate #104

Stable version with tests for rOpenSci submission

• Includes tests with 80% code coverage
• Examples for every function
• Improved README with status badges
• JOSS-format paper.md draft
• Submitted to rOpensci for software review

bug & documentation fixes in relative quantification

v0.2.1-beta

calculate_efficiency warning correct, fixes #80

relative quantification with delta Cq and delta delta Cq

Upgraded features for relative quantification, new vignettes to explain these, and gave functions more helpful names such as calculate... as well as create...

• lay out and display 96/384-well plates for easy experimental setup (label_plate_rowcol, create_blank_plate, ...)
• read-in Cq and raw data from Roche LightCycler machines with single-channel fluorescence (read_lightcycler_1colour_cq, read_lightcycler_1colour_raw)
• delta Cq: normalization/ relative quantification of Cq data to one or more reference targets by delta count method (calculate_normcq, calculate_deltacq_bysampleid)
• delta delta Cq: normalization of delta Cq data across multiple samples (calculate_deltadeltacq_bytargetid)
• calibration of primer sets including estimating efficiencies and visualization of curves (calculate_efficiency, and see vignettes)
• visualization of amplification and melt curves (calculate_drdt_plate, and see vignettes)

version 0.1 alpha with Sample, Probe, Ct

Code that used tidyqpcr before April 2020 should work using this release. The required variables for a plate plan analysis were:

• Sample (later replaced by SampleID)
• Probe (later replaced by TargetID)
• Type (still there)
• Ct (later replaced

We packaged this into a release to enable users to re-run old analysis scripts without rewriting.